RetrogeneDB ID: retro_ocun_518

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:90501830..90502228(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021731
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSOCUG00000002997
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5-like [Source:HGNC Symbol;Acc:23366]

Sequence

>retro_ocun_518
ATGGCCCGGAACACCCTGTCTTCACGCTTCCGCTGGGTGGATATCCACGAGTCTGGCGAGAACAAATTCGTGGACGAGCA
GGAGGTGGTGGCGGCAGTGGCGGGAGAGCCAGGCCCGGACCCTAGCGAGGTGGACGGGCTCCTGTGGCAAGGGGACATGC
TTCAGGCGTTCCACGCCACCTTGCGGAACTCTCTGGTCAACACCAAGAACCAGGCTGTGAAGGAGCAAGACCAGGGCGTG
GTGCTGAAGGTGCTCACTAACTTCAAGATCAGCGAAATTGAGCAGGCTGTGCAGTCTCTGGACAGAAATGGCATTGACTT
GTTAATGAAGTACATTTATAAAGGTTTGAGAAGCTCACAGAAAACAGCAGTGCAGTGCTGCTGCAGTGGCATGAAAAG

Alignment

ORF - retro_ocun_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.31 %
• Parental protein coverage: 86.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARNTLSSRFRRVDIDEFDENKFVDEQEEAAAAAGEPGPDPSEVDGLLRQWDMLRAFHAALRNSPVNTKN
          MARNTLSSRFR.VDI.E..ENKFVDEQE..AA.AGEPGPDPSEVDGLL.Q.DML.AFHA.LRNS.VNTKN
Retrocopy MARNTLSSRFRWVDIHESGENKFVDEQEVVAAVAGEPGPDPSEVDGLLWQGDMLQAFHATLRNSLVNTKN

Parental  QAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGIDLLMKYIYKG-FEKPTENSSAVLLQWHEK
          QAVKE..QGVVLKVLTNFK.SEIEQAVQSLDRNGIDLLMKYIYKG.FEK.TENSSAVLLQWHEK
Retrocopy QAVKEQDQGVVLKVLTNFKISEIEQAVQSLDRNGIDLLMKYIYKG<FEKLTENSSAVLLQWHEK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.44 RPM	23.90 RPM
SRP017611_kidney	0.30 RPM	17.23 RPM
SRP017611_liver	0.15 RPM	5.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_518 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_518 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518 ,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,